Endogenous respiration processes of nitrifying/denitrifying bacteria under aerobic and anoxic conditions were investigated in a batch study using three identical bioreactors of size 5 L. The rate of digestion of microbial protoplasm was determined through the oxidation of cell tissue and the formation of new cellular materials using the Volatile Suspended Solids (VSS) method. Chemical Oxygen Demand (COD), ammonia, nitrate and VSS were monitored simultaneously at different sludge age. Three exponential phases of metabolism, starvation and death were observed duringVSS reduction in both the aerobic and anoxic digestion. In the aerobic digestion, the average endogenous decay coefficient of volatile suspended solids was 0.055 L day-1 with a 95 confidence limit of 0.017 whereas 0.053 L day-1 was observed for anoxic digestion with a 95 confidence limit of 0.038 at 25±1°C. Results show that anoxic digestion has a slightly reduced decay rate than aerobic digestion. Therefore, the characterization of biomass and determination of stoichiometry coefficients is essential for understanding the activities of microbes in treatment processes. © 2015 Academic Journals Inc.